Reference SNP(refSNP) Cluster Report: rs2073820

Reference SNP(refSNP) Cluster Report: rs2073820

refSNP ID: rs2073820
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_004188.3:c.511-271C>T
NT_035014.4:g.2641117C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss77557875 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2073820 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss2988275	YUSUKE\|IMS-JST000408	fwd/T	A/G	ttgcctcatctagaggcggaatagcccagt	gttaagagctgggagttggccgaagctggg	05/24/01	10/10/03	96	Genomic	unknown
ss43438390	ABI\|hCV2535212	rev/B	C/T	cccagcttcggccaactcccagctcttaac	actgggctattcagcctctagatgaggcaa	07/18/05	11/03/06	126	Genomic	unknown
ss76590242	AFFY\|AFFY_6_1M_SNP_A-8451317	rev/B	C/T	actcccagctcttaac	actgggctattccgcc	08/28/07	08/30/07	129	Genomic	unknown
ss77557875	HGSV\|Cor12156_SNV_20070510.chr9_132893731	rev/B	C/T	cccagcttcggccaactcccagctcttaac	actgggctattcagcctctagatgaggcaa	10/09/07	10/13/07	129	Genomic	unknown

Fasta sequence (Legend)

 TGCCGCAGAT GTCACAGGCG AAGGGCCGGG TCCCACTATG GGAGCGTCGC ACATGCACTT
 CGAGCCCGTG AGGGGTGGAG AAGACCTGGG AGCAGGGGCA GCATGTGAGG CCACTGGGGG
 CTGCGGTGAC AGGGACAGGC CTGGGGTCCC ATGGTCTCTT CCATGCCCAG CTCTGGCCAA
 GGCTGGGTAC ACAGAGTAAG GGGCACTGGA TTGCCAGTTC TGCTGCTTGC TTGCTGTGTG
 TCCCAGGGAG GTCCGTTTGC CTCTCTGTGG CTCAGTCTCC CTTCTACAAA GTTGGATGTG
 AGAGAGGGGA TCTGGAGGCC CCTCCTTGCC TCATCTAGAG GCTGAATAGC CCAGT
 R
 GTTAAGAGCT GGGAGTTGGC CGAAGCTGGG TTTGAATGCT GGTTCTGATA TCTACTTGCT
 GTCTGATCCT GGAAAAGTGA CTTAACCTCT CTGAACCTTA ACCTTTCATC TGACTCTGGC
 ACTCATGCCT GTCAATTGCT TAGCACAGGG CCAGGCACGT GGTCAGAGCT CAATGAATGG
 TGATGAGGAT GAACGTTTTG AATCCTTAAT CCCACCAGAG CCCCAACATT CACAGCACAG
 AGAACGCCCA GAGCTGCCAG TGAGTTGAGA GGGAGTGCGG AGAGGAGGGC CCAGGTGCCC
 ACCACACCCC CCGCTGCCCA CCTTGTTGCA CTTCACACAG TGGTACGCAT CCATGCCTGG
 GGAGTAGCGG AGGCTGAAGT C

GeneView

GeneView via analysis of contig annotation: GFI1B growth factor independent 1B transcription repressor

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_035014->NM_004188

function

HuRef

NW_001839241->NM_004188

function

Celera

NW_924573->NM_004188

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_035014->NM_004188->NP_004179	2641117	forward	intron

HuRef	NW_001839241->NM_004188->NP_004179	596158	reverse	intron

Celera	NW_924573->NM_004188->NP_004179	19893747	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2073820 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839241.2	596158	105357856	plus	G	alt_assembly_8	HuRef	HuRef	view	300
9	NW_924573.1	19893747	106405916	minus	C	alt_assembly_1	Celera	Celera	view	300
9	NT_035014.4	2641117	134853998	minus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
AC000393.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AL593851.6

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss43438390	HapMap-HCB	Asian	90	IG	0.244	0.444	0.311	0.479	0.467	0.533

	HapMap-JPT	Asian	88	IG	0.159	0.477	0.364	1.000	0.398	0.602

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.067	0.917	0.025	0.050	0.950

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.402+/-0.199	180	150	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .